AMBER ff99SB on NAMD

From: Luis Cunha (Luis.Cunha_at_mssm.edu)
Date: Sat Nov 01 2008 - 19:43:30 CDT

hi,
I'm doing a simulation on NAMD using the ff99SB AMBER force field. According to NAMD instructions to use the AMBER ff with NAMD (http://www.ks.uiuc.edu/Research/namd/2.6/ug/node15.html) the following NAMD parameters:

rigidTolerance 0.0001
1-4scaling 1.0

    should be changed to AMBER compatible values:

rigidTolerance 0.0005
1-4scaling 0.83333

However, while simulations with the first set maintain the protein conformation, simulations with the second set (recommended when using amber ff) destroy a few helices(not all!; the helix residues break apart into a random coil).

Has anyone experienced this problem? What am I doing wrong?

Thank you in advance for your help,

Luis Cunha, PhD
Dept. of Human Genetics
Mount Sinai School of Medicine of the New York University

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